Index

_

__call__() (mlatom.data.h5md method)

A

add_atom_from_xyz_string() (mlatom.data.molecule method) add_scalar_properties() (mlatom.data.molecular_database method) add_scalar_properties_from_file() (mlatom.data.molecular_database method) add_scalar_property() (mlatom.data.molecule method) add_xyz_derivative_properties() (mlatom.data.molecular_database method) add_xyz_derivative_properties_from_file() (mlatom.data.molecular_database method) add_xyz_derivative_property() (mlatom.data.molecule method)

add_xyz_vectorial_properties() (mlatom.data.molecular_database method) add_xyz_vectorial_properties_from_file() (mlatom.data.molecular_database method) add_xyz_vectorial_property() (mlatom.data.molecule method) ani() (in module mlatom.models) append() (mlatom.data.molecular_database method) atom (class in mlatom.data) atomic_numbers (mlatom.data.molecular_database property) (mlatom.data.molecule property)

C

calculate_validation_loss() (mlatom.models.ml_model method) cell (mlatom.data.molecule property) cell_coordinates (mlatom.data.molecule property) charge (mlatom.data.molecule attribute) charges (mlatom.data.molecular_database property) close() (mlatom.data.h5md method)

config_multiprocessing() (mlatom.models.methods method) (mlatom.models.model method) copy() (mlatom.data.atom method) (mlatom.data.molecular_database method) (mlatom.data.molecule method) (mlatom.models.hyperparameter method) (mlatom.models.hyperparameters method)

D

dmc (class in mlatom.simulations) dpmd() (in module mlatom.models) dump() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method) (mlatom.models.ml_model method) (mlatom.models.model_tree_node method)

E

element_symbols (mlatom.data.molecular_database property) (mlatom.data.molecule property)

energy_gaps (mlatom.data.molecule property) excitation_energies (mlatom.data.molecule property) export() (mlatom.data.h5md method)

F

freq (class in mlatom.simulations) from_numpy() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method) from_smiles_file() (mlatom.data.molecular_database class method) from_smiles_string() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method)

from_xyz_file() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method) from_xyz_string() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method)

G

gap() (in module mlatom.models) generate_initial_conditions() (in module mlatom.initial_conditions) generate_model_dict() (mlatom.models.kreg method) (mlatom.models.ml_model method) get_properties() (mlatom.data.molecular_database method) get_xyz_derivative_properties() (mlatom.data.molecular_database method)

get_xyz_string() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method) get_xyz_vectorial_properties() (mlatom.data.molecular_database method) get_xyzvib_string() (mlatom.data.molecule method) get_zpe() (mlatom.simulations.dmc method)

H

h5 (mlatom.data.h5md attribute) h5md (class in mlatom.data)

hyperparameter (class in mlatom.models) hyperparameters (class in mlatom.models)

I

id (mlatom.data.molecule attribute)

ids (mlatom.data.molecular_database property)

K

kinetic_energy (mlatom.data.molecule property)

kreg (class in mlatom.models)

L

load() (mlatom.data.molecular_database class method) (mlatom.data.molecular_trajectory method) (mlatom.simulations.dmc method)

M

mace() (in module mlatom.models) map_to_unicell() (mlatom.data.molecule method) md (class in mlatom.md) md.Andersen_thermostat (class in mlatom.md) md.Nose_Hoover_thermostat (class in mlatom.md) methods (class in mlatom.models) ml_model (class in mlatom.models) mlatom.data module mlatom.initial_conditions module mlatom.interfaces module mlatom.md module mlatom.models module, [1], [2], [3] mlatom.namd module

mlatom.simulations module model (class in mlatom.models) model_tree_node (class in mlatom.models) module mlatom.data mlatom.initial_conditions mlatom.interfaces mlatom.md mlatom.models, [1], [2], [3] mlatom.namd mlatom.simulations molecular_database (class in mlatom.data) molecular_trajectory (class in mlatom.data) molecule (class in mlatom.data) multiplicities (mlatom.data.molecular_database property) multiplicity (mlatom.data.molecule attribute)

N

nthreads (mlatom.models.methods property)

nuclear_masses (mlatom.data.molecular_database property)

O

optimize_geometry (class in mlatom.simulations)

optimize_hyperparameters() (mlatom.models.ml_model method)

P

pbc (mlatom.data.molecule property) physnet() (in module mlatom.models) predict() (mlatom.models.kreg method) (mlatom.models.methods method) (mlatom.models.ml_model method) (mlatom.models.model method) (mlatom.models.model_tree_node method)

proliferate() (mlatom.data.molecular_database method) (mlatom.data.molecule method)

R

read_from_numpy() (mlatom.data.molecular_database method) (mlatom.data.molecule method) read_from_smiles_file() (mlatom.data.molecular_database method) read_from_smiles_string() (mlatom.data.molecular_database method) (mlatom.data.molecule method)

read_from_xyz_file() (mlatom.data.molecular_database method) (mlatom.data.molecule method) read_from_xyz_string() (mlatom.data.molecular_database method) (mlatom.data.molecule method) reset() (mlatom.models.ml_model method) run() (mlatom.simulations.dmc method)

S

set_properties() (mlatom.data.molecular_database method) sgdml() (in module mlatom.models) smiles (mlatom.data.molecular_database property) (mlatom.data.molecule property)

split() (mlatom.data.molecular_database method) state_energies (mlatom.data.molecule property) state_gradients (mlatom.data.molecule property) surface_hopping_md (class in mlatom.namd)

T

thermochemistry (class in mlatom.simulations) to_database() (mlatom.data.molecular_trajectory method)

train() (mlatom.models.kreg method) (mlatom.models.ml_model method)

U

update() (mlatom.models.hyperparameter method)

V

view() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method)

W

write() (mlatom.data.h5md method) write_file_energy_gradients() (mlatom.data.molecular_database method) write_file_with_hessian() (mlatom.data.molecular_database method) write_file_with_properties() (mlatom.data.molecular_database method)

write_file_with_smiles() (mlatom.data.molecular_database method) write_file_with_xyz_coordinates() (mlatom.data.molecular_database method) (mlatom.data.molecule method) write_file_with_xyz_derivative_properties() (mlatom.data.molecular_database method) write_file_with_xyz_vectorial_properties() (mlatom.data.molecular_database method)

X

xyz_coordinates (mlatom.data.molecular_database property) (mlatom.data.molecule property)